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Seems like the Xilinx tools you are using is modifying the net names hence RC cannot annotate them. The good news is net annotation is not nearly as important since it is not what is conisdered a 'synthesis-invariant' point. In other words, tools are frequently not guaranteed to be able to keep or predict all net names. Furthermore, net activity will be recomputed by propagating the activity of the sequential outputs your successfully annotated. In fact, if all you care about is static power and not power/toggle vs timing, then recommendation would be to just do

write_tcf -boundary_only -hierarchical . . .

and use the TCF from that point since it will read faster and it will no longer have the nets in it.